SureshKumar's Bioinformatics Blog

I am Suresh Kumar Sampathrajan. I have completed my PhD degree in bioinformatics from the University of Vienna, Austria in the year 2010. If you want to know more about me and my research,please click the menus at the top.

I have started this bioinformatics blog mainly for undegraduate and postgraduate students of bioinformatics. This blog will serve as an open resource material for the students and for those who wish to know about bionformatics. This blog contains video tutorials, tips, bioinformatics software downloads, articles on bioinformatics and career opportunities.

Computational tools for Glycomics Studies

Sugars are involved in almost every aspect of biology, from recognising pathogens and to blood clotting.The glycome's basic building blocks are far more numerous and varied than the four letters of the DNA alphabet or the score of amino acids that make proteins.In the late 1980s, when researchers isolated the first gene for a glycosyl transferase, an enzyme that adds sugars to fats and proteins. The discovery gave scientists the first opportunity to study this process, which is usually called glycoslyation, by manipulating the activity of such enzymes.


Fig: Carbohydrate only (no protein) - PDB id:2HYA


Glycomics, or glycobiology is a discipline of biology that deals with the structure and function of oligosaccharides (chains of sugars). The identity of the entirety of carbohydrates in an organism is thus collectively referred to as the glycome.The progressing glycomics projects will dramatically accelerate the understanding of the roles of carbohydrates in cell communication and hopefully lead to novel therapeutic approaches for treatment of human disease

The Functional Glycomics Gateway is a comprehensive and free online resource that is the result of a collaboration between the Consortium for Functional Glycomics (CFG) and Nature Publishing Group. It is aimed at keeping you abreast of developments in the emerging field of functional glycomics.

http://www.functionalglycomics.org/static/index.shtml

For annotation and/or cross-reference carbohydrate-related data collections which will allow us to find important data for compounds of interest in a compact and well-structured representation

http://www.glycosciences.de/sweetdb/

Many pdb-files contain carbohydrate structures. Since there is not such a standard nomenclature like it exists for amino acids, it is difficult to find the carbohydrate information. Sometimes entire oligosaccharides are encoded in one single residue. Information about carbohydrate linkages is often missing, and if it is present, it is not in a unique format and therefore also difficult to find.pdb2linucs automatically extracts carbohydrate information from pdb-files .

http://www.dkfz-heidelberg.de/spec/pdb2linucs/


GlycoSuite comprises GlycoSuiteDB, the leading curated and annotated glycan database, and new bioinformatic tools which interface mass spectrometric data with the database.

https://glycosuite.proteomesystems.com/glycosuite/glycodb

A Complex Carbohydrate Structure Database, also known as CarbBank is available . But, due to lack of funding it is no longer updated.

http://www.boc.chem.uu.nl/sugabase/carbbank.html


Protein druggability prediction

The availability of structural data, especially of proteins complexed to small molecule ligands, has enabled numerous analyses that attempt to understand and predict the forces that govern molecular recognition and ligand binding. Successful drug development requires a disease target that plays a vital role in the causation and progression of the disease phenotype and that can be modulated with a drug molecule.

One approach for evaluating protein druggability is to analyze the genome on the basis of sequence homology to known therapeutic targets.

Another approach which rely on on the 3D structure of the protein target. Systematic analyses of protein srufaces in the search for binding pockets that have high potential to bind small drug like compuunds with high affinity.

To identify all possible binding sites on a protien surface based on algorithms broadly classified into

(i) Geometry-based

Tools based on geometry based alogirthm

Binding site prediction for malate dehydrogenase (PDB: 2cmd).

(ii)Energy based algorithms

Tools based on Energy based algorithms

  • GRID
  • vdW-FT
  • Drugsite

Useful online resources for cancer target finding and analysis


Collection of cancer genes based on mutation data


http://www.sanger.ac.uk/genetics/CGP/Census/



Repository of microarray data from cancer genomics publication

www.broad.mit.edu/cgi-bin/cancer/datasets.cgi



Respository of cytogenetic abnormalities in human cancer

http://www.progenetix.de/



Respository of cytogenetic abnormalities in human cancer

www.ncbi.nlm.nih.gov/sky



Validated SBNPs in cancer genes

http://snp500cancer.nci.nih.gov/home.cfm

BioMed -Bioinformatics search engine


PubMed is the free public interface to MEDLINE. It provides access to bibliographic information in MEDLINE as well as additional life science journals.
Searching articles on PubMed requires some skill and more over it does not support some of search strings like popular search engines (Google and Yahoo).

Eventhough we can search through Google Scholar it gives many false positive results. But, Google provides us to customise our own search engine through google co-op. Through this we can create our own search engine on our interested topic.

I have created a search engine for bioinformatics through Google Co-op, this search engine searches only bioinformatics related journals and it has less false positive results. But this BioMed search engine is still in beta version and it requires further improvement.

You can access the BioMed - Search engine for bioinformatics by clicking here.

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